Hey Jim,
sorry, I don’t have any experience with the QCW frame because I did not yet assemble mine yet. I am not sure if I will use it at all, probably just for testing since I plan to weld a sophisticated machine base from steel profiles instead. But I would say if the QCW frame is not “square” (rectangular), then you have a problem.
Maybe you can tweak the holes in the four end cubes. If not, I think in the end you would try to solve it by disassembing everything and filing the ends of the beams so that they end up “square”. Or send it back until you get a “square” one.